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I have written the CWL code which runs the Rscript command in the docker container. I have two files of cwl and yaml and run them by the command: 

cwltool --debug a_code.cwl a_input.yaml

I get the output which said that the process status is success but there is no output file and in the result "output": null is reported. I want to know if there is a method to find that the Rscript file has run on the docker successfully. I want actually know about the reason that the output files are null.

The final part of the result is:

[job a_code.cwl] {
    "output": null, 
    "errorFile": null
}
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
Removing intermediate output directory /tmp/tmpCG9Xs1
Removing intermediate output directory /tmp/tmpCG9Xs1
{
    "output": null, 
    "errorFile": null
}
Final process status is success
Final process status is success

R code: 

library(cummeRbund)
cuff<-readCufflinks( dbFile = "cuffData.db", gtfFile = NULL, runInfoFile = "run.info", repTableFile = "read_groups.info", geneFPKM = "genes.fpkm_trac .... )
#setwd("/scripts")
sink("cuff.txt")
print(cuff)
sink()

My cwl file code is: 

class: CommandLineTool
cwlVersion: v1.0
id: cummerbund
baseCommand:
  - Rscript
inputs:
  - id: Rfile
    type: File?
    inputBinding:
      position: 0
  - id: cuffdiffout
    type: 'File[]?'
    inputBinding:
      position: 1
  - id: errorout
    type: File?
    inputBinding:
      position: 99
      prefix: 2>
      valueFrom: |
        error.txt
outputs:
  - id: output
    type: File?
    outputBinding:
      glob: cuff.txt
  - id: errorFile
    type: File?
    outputBinding:
      glob: error.txt
label: cummerbund
requirements:
  - class: DockerRequirement
    dockerPull: cummerbund_0

my input file (yaml file) is:

 inputs:
    Rfile:
      basename: run_cummeR.R
      class: File
      nameext: .R
      nameroot: run_cummeR
      path: run_cummeR.R
    cuffdiffout:
      - class: File
        path: cuffData.db
      - class: File
        path: genes.fpkm_tracking
      - class: File
        path: read_groups.info
      - class: File
        path: genes.count_tracking
      - class: File
        path: genes.read_group_tracking
      - class: File
        path: isoforms.fpkm_tracking
      - class: File
        path: isoforms.read_group_tracking
      - class: File
        path: isoforms.count_tracking
      - class: File
        path: isoform_exp.diff
      - class: File
        path: gene_exp.diff
    errorout:
      - class: File
        path: error.txt

Also, this is my Dockerfile for creating image:

FROM r-base
COPY . /scripts
RUN apt-get update
RUN apt-get install -y \
    libcurl4-openssl-dev\
    libssl-dev\
    libmariadb-client-lgpl-dev\
    libmariadbclient-dev\
    libxml2-dev\
    r-cran-plyr\
    r-cran-reshape2
WORKDIR /scripts
RUN Rscript /scripts/build.R
ENTRYPOINT /bin/bash
shadi
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  • How are you running the docker image? The output file may be generated inside the docker instance but it will not appear on your local file system unless you use volumes. https://stackoverflow.com/questions/47831774/docker-run-with-volume – Emer Feb 19 '18 at 19:29
  • I checked it. I run the docker by: docker run -i -t --rm cummerbund_0:latest and also I checked by the command docker cp 0f42fb5ad89e:/scripts/cuff.txt shafighi/CWLs/ to move the file if exists. but there is no file. I will add my docker file for creating image to the post too. – shadi Feb 19 '18 at 19:33

1 Answers1

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I got the answer! There were some problems in my program. 1. The docker was not pulled correctly then the cwl couldn't produce any output.
2. The inputs and outputs were not defined mandatory. So I got the success status in the case which I did not have proper inputs and output.

shadi
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